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62-487: 104472715 n/a ENSG00000224078 n/a n a n/a n/a n/a n/a n/a UBE3A-ATS/Ube3a-ATS (human/mouse), otherwise known as ubiquitin ligase E3A-ATS , is the name for the antisense DNA strand that is transcribed as part of a larger transcript called LNCAT (large non-coding antisense transcript) at the Ube3a locus. The Ube3a locus is imprinted and in the central nervous system expressed only from

124-581: A multi-protein complex , is, in general, responsible for targeting ubiquitination to specific substrate proteins. The ubiquitylation reaction proceeds in three or four steps depending on the mechanism of action of the E3 ubiquitin ligase. In the conserved first step, an E1 cysteine residue attacks the ATP-activated C-terminal glycine on ubiquitin, resulting in a thioester Ub-S-E1 complex. The energy from ATP and diphosphate hydrolysis drives

186-491: A post-translational modification such as phosphorylation of a tyrosine , serine or threonine residue. In this case, the ubiquitin ligase exclusively recognizes the phosphorylated version of the substrate due to stabilization within the binding site . For example, FBW7 , the F-box substrate recognition unit of an SCF ubiquitin ligase, stabilizes a phosphorylated substrate by hydrogen binding its arginine residues to

248-424: A different extent by their appropriate ubiquitin ligase (N-recognin), influencing the half-life of the protein. For instance, positively charged ( Arg , Lys , His ) and bulky hydrophobic amino acids ( Phe , Trp , Tyr , Leu , Ile ) are recognized preferentially and thus considered destabilizing degrons since they allow faster degradation of their proteins. A degron can be converted into its active form by

310-467: A gene called UBE3A that, when mutated or absent, likely causes the characteristic features of this condition. People normally have two copies of the UBE3A gene, one from each parent. Both copies of this gene are active in many of the body's tissues. In the brain, however, only the copy inherited from a person's mother (the maternal copy) is active. If the maternal copy is lost because of a chromosomal change or

372-455: A gene mutation, a person will have no working copies of the UBE3A gene in the brain. In most cases (about 70%) , people with Angelman syndrome have a deletion in the maternal copy of chromosome 15. This chromosomal change deletes the region of chromosome 15 that includes the UBE3A gene. Because the copy of the UBE3A gene inherited from a person's father (the paternal copy) is normally inactive in

434-501: A larger long arm (the "q" arm) that is gene rich, spanning about 83 million base pairs. The human leukocyte antigen gene for β2-microglobulin is found on chromosome 15, as well as the FBN1 gene, coding for both fibrillin-1 (a protein critical to the proper functioning of connective tissue), and asprosin (a small protein produced from part of the transcribed FBN1 gene mRNA), which is involved in fat metabolism. The following are some of

496-406: A lower bound on the total number of human protein-coding genes. The following is a partial list of genes on human chromosome 15. For complete list, see the link in the infobox on the right. The following conditions are caused by mutations in chromosome 15. Two of the conditions ( Angelman syndrome and Prader–Willi syndrome ) involve a loss of gene activity in the same part of chromosome 15,

558-469: A mutation in a gene other than UBE3A. These genetic changes can abnormally inactivate the UBE3A gene. Angelman syndrome can be hereditary, as evidenced by one case where a patient became pregnant with a daughter who also had the condition. The main characteristics of this condition include polyphagia (extreme, insatiable appetite), mild to moderate developmental delay, hypogonadism resulting in delayed to no puberty, and hypotonia . Prader-Willi syndrome

620-785: A result, a number of these proteins are involved in a variety of cancers, including famously MDM2, BRCA1 , and Von Hippel-Lindau tumor suppressor . For example, a mutation of MDM2 has been found in stomach cancer , renal cell carcinoma , and liver cancer (amongst others) to deregulate MDM2 concentrations by increasing its promoter’s affinity for the Sp1 transcription factor , causing increased transcription of MDM2 mRNA. Several proteomics-based experimental techniques are available for identifying E3 ubiquitin ligase-substrate pairs, such as proximity-dependent biotin identification (BioID), ubiquitin ligase-substrate trapping, and tandem ubiquitin-binding entities (TUBEs). Chromosome 15 Chromosome 15

682-533: A road wide enough for only one car. A smart car is traveling from one direction, and a plough from the other direction, eventually colliding. After the collision, the plough pushes the smart car backwards, as it continues to travel forward. In the collision model for Ube3a/Ube3a-ATS , RNA polymerases (RNAPs) travel towards each other along the sense and antisense templates during transcription. The sense and antisense templates overlap for Ube3a and Ube3a-ATS . The two transcription bubbles will collide head-on, and

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744-414: Is hydroxylated . Under hypoxia , on the other hand, HIF-a is not hydroxylated, evades ubiquitination and thus operates in the cell at higher concentrations which can initiate transcriptional response to hypoxia. Another example of small molecule control of protein degradation is phytohormone auxin in plants. Auxin binds to TIR1 (the substrate recognition domain of SCF ubiquitin ligase) increasing

806-442: Is caused by the loss of active genes in a specific part of chromosome 15, the 15q11-q13 region. People normally have two copies of this chromosome in each cell, one copy from each parent. Prader–Willi syndrome occurs when the paternal copy is partly or entirely missing. In about 70% of cases, Prader–Willi syndrome occurs when the 15q11-q13 region of the paternal chromosome 15 is deleted. The genes in this region are normally active on

868-536: Is found in the cytoplasm. A specific imprinting center cluster was thought to control the differential expression of Ube3a-ATS on the maternal and paternal alleles . There are two regions in the imprinting centers (ICs) that exist associated with AS and PWS- the AS-IC and the PWS-IC. These imprinting centers are control regions that dictate whether surrounding genes and regions can be expressed and are found on both

930-624: Is further processed and spliced. Reviewed in Trends in Neurosci . Located next to the U-exon promoter region is Snrpn/Snurf which can be alternatively spliced into either Snrpn or Snurf in humans (in mice this remains as one bicistronic transcript). Snrpn codes for a protein of unknown function which localizes to the cell nucleus . Snurf codes for a small nuclear ribonucleoprotein . While most of these proteins are involved in splicing ,

992-403: Is generally not hereditary. A specific chromosomal change called an isodicentric chromosome 15 (IDIC15) (also known by a number of other names ) can affect growth and development. The patient possesses an "extra" or "marker" chromosome. This small extra chromosome is made up of genetic material from chromosome 15 that has been abnormally duplicated (copied) and attached end-to-end. In some cases,

1054-434: Is one of the 23 pairs of chromosomes in humans . People normally have two copies of this chromosome. Chromosome 15 spans about 99.7 million base pairs (the building material of DNA ) and represents between 3% and 3.5% of the total DNA in cells . Chromosome 15 is an acrocentric chromosome, with a very small short arm (the "p" arm, for "petite"), which contains few protein coding genes among its 19 million base pairs. It has

1116-634: Is possible that the maternal Ube3a mRNA interacts with the paternal Ube3a-ATS RNA and decreases the stability of both of these transcripts. When only Ube3a-ATS is made without Ube3a , the Ube3a-ATS becomes more stable. Another study has suggested that Ube3a-ATS expression does not occur in imprinted regions. In situ hybridizations did not reveal Ube3a-ATS in Purkinje cells or hippocampal neurons. However, other upstream exons that correspond to Snurf / Snrpn were expressed, indicating that

1178-419: Is referred to as an E3, and operates in conjunction with an E1 ubiquitin-activating enzyme and an E2 ubiquitin-conjugating enzyme . There is one major E1 enzyme, shared by all ubiquitin ligases, that uses ATP to activate ubiquitin for conjugation and transfers it to an E2 enzyme. The E2 enzyme interacts with a specific E3 partner and transfers the ubiquitin to the target protein . The E3, which may be

1240-443: Is supported by several studies where preventing methylation of the PWS-IC by knocking out methyl transferases in embryonic stem cells results in biallelic expression of Ube3a-ATS and silencing of Ube3a on the maternal allele. However, methylation is not the only process involved in preventing the expression of the maternal Ube3a-ATS . It is expected that the imprinting domains interact with other proteins, which contribute to

1302-455: The ERAD pathway, on the other hand, are recognized by Fbs1 and Fbs2, mammalian F-box proteins of E3 ligases SCF and SCF . These recognition domains have small hydrophobic pockets allowing them to bind high- mannose containing glycans . In addition to linear degrons , the E3 ligase can in some cases also recognize structural motifs on the substrate. In this case, the 3D motif can allow

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1364-551: The Ube3a-ATS of LNCAT silences the paternal Ube3a - the collision model, the RNA-DNA interaction model, and the double stranded RNA interference model. While these models have not been demonstrated directly for Ube3a/Ube3a-ATS , they are considered plausible based on evidence for the silencing of other natural antisense transcripts by these methods. However, the collision model, due to most recent supporting studies, appears most likely. The collision model can be thought of as

1426-547: The cell , and from other (ubiquitination-inactive) forms of the same protein. This can be achieved by different mechanisms, most of which involve recognition of degrons : specific short amino acid sequences or chemical motifs on the substrate. Proteolytic cleavage can lead to exposure of residues at the N-terminus of a protein. According to the N-end rule , different N-terminal amino acids (or N-degrons) are recognized to

1488-578: The imprinting center are found in the U-exon region. The promoter region is imperative, as deletion of this area abolishes Ube3a-ATS transcription . Near the promoter is the PWS-IC and about 35 kbs upstream of the PWS-IC is the AS-IC . These two regions are thought to control the expression of the entire LNCAT strand. Starting at the promoter, the entire transcript can be transcribed and after transcription

1550-484: The replication fork . However, their mechanism of action in activating the paternal Ube3a is not yet known, but may involve transcriptional interference with Ube3a-ATS , as Ube3a-ATS transcripts decreased after drug treatment. The group specifically chose to study topotecan , which was the most effective at a low nanomolar range and is already Food and Drug Administration approved for treating several types of cancers. Ubiquitin ligase The ubiquitin ligase

1612-502: The silencing of LNCAT and Ube3a-ATS on the maternal allele. For example, when MECP2 is knocked out, such as in Rett syndrome patients, Ube3a-ATS is biallelically expressed, decreasing expression of Ube3a from the maternal allele. Only one RNA polymerase (RNAP) can transcribe along a part of the template at a time. When two RNAPs are transcribing in head on directions, a collision can occur. This can result in stalling of both of

1674-434: The 15q11.2-q13.1 region. This discovery provided the first evidence in humans that something beyond genes could determine how the genes are expressed . The main characteristics of Angelman syndrome are severe intellectual disability, ataxia , lack of speech, and excessively happy demeanor. Angelman syndrome results from a loss of gene activity in a specific part of chromosome 15, the 15q11-q13 region. This region contains

1736-618: The E1 and E2. The E3 ligases are classified into four families: HECT, RING-finger, U-box, and PHD-finger. The RING-finger E3 ligases are the largest family and contain ligases such as the anaphase-promoting complex (APC) and the SCF complex ( Skp1 - Cullin -F-box protein complex). SCF complexes consist of four proteins: Rbx1, Cul1, Skp1, which are invariant among SCF complexes, and an F-box protein, which varies. Around 70 human F-box proteins have been identified. F-box proteins contain an F-box, which binds

1798-580: The E3 ligase MDM2 ubiquitylates p53 either for degradation (K48 polyubiquitin chain), or for nuclear export (monoubiquitylation). These events occur in a concentration dependent fashion, suggesting that modulating E3 ligase concentration is a cellular regulatory strategy for controlling protein homeostasis and localization. Ubiquitin ligases are the final, and potentially the most important determinant of substrate specificity in ubiquitination of proteins . The ligases must simultaneously distinguish their protein substrate from thousands of other proteins in

1860-745: The N-terminal methionine are used in chains in vivo. Monoubiquitination has been linked to membrane protein endocytosis pathways. For example, phosphorylation of the Tyrosine at position 1045 in the Epidermal Growth Factor Receptor (EGFR) can recruit the RING type E3 ligase c-Cbl, via an SH2 domain . C-Cbl monoubiquitylates EGFR, signaling for its internalization and trafficking to the lysosome. Monoubiquitination also can regulate cytosolic protein localization. For example,

1922-404: The PWS-IC has been deleted, expression of the Ube3a-ATS is decreased. In the central neural system, Ube3a-ATS is preferentially expressed from the paternal allele where the PWS-IC is not methylated. On the other hand, on the maternal allele, where the PWS-IC is methylated, Ube3a-ATS is not expressed, suggesting that the methylation of the PWS-IC somehow prevents Ube3a-ATS expression. This

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1984-472: The RNAP transcribing the Ube3a-ATS , being the plough, will push the RNAP transcribing the Ube3a (smart car), backwards and eventually off of the template. This prevents complete transcription of Ube3a. The support for this model comes from two recent studies. The first study looked at transcription of genes on sense strands that were overlapped by genes being expressed on the antisense strand . The longer

2046-457: The RNAPs, backtracking of one RNAP, or falling off of the template. In this case, the RNAP transcribing the paternal UBE3A-ATS competes with the RNAP transcribing UBE3A and pushes it off of the template, preventing UBE3A transcription and allowing UBE3A-ATS transcription. Arrows show the direction of transcription. Reviewed in Trends in Neurosci .]] There are currently three models that explain how

2108-523: The affinity of TIR1 for its substrates (transcriptional repressors : Aux/IAA), and promoting their degradation. In addition to recognizing amino acids, ubiquitin ligases can also detect unusual features on substrates that serve as signals for their destruction. For example, San1 ( Sir antagonist 1 ), a nuclear protein quality control in yeast , has a disordered substrate binding domain , which allows it to bind to hydrophobic domains of misfolded proteins . Misfolded or excess unassembled glycoproteins of

2170-430: The brain, a deletion in the maternal chromosome 15 results in no active copies of the UBE3A gene in the brain. In 3% to 7% of cases, Angelman syndrome occurs when a person has two copies of the paternal chromosome 15 instead of one copy from each parent. This phenomenon is called paternal uniparental disomy (UPD). People with paternal UPD for chromosome 15 have two copies of the UBE3A gene, but they are both inherited from

2232-429: The collision model could still be occurring. Thus further research is still required. Several studies have attempted to utilize the possibility of controlling Ube3a expression through Ube3a-ATS . In AS, the paternal PWS-IC is not methylated, supposedly allowing Ube3a-ATS expression. Therefore, if methylation of the PWS-IC were possible, Ube3a-ATS transcription could be prohibited, allowing Ube3a expression from

2294-520: The drug topotecan , administered to mice suffering from AS, activated expression of the paternal Ube3a gene by lowering the transcription of Ube3a-ATS . The human UBE3A-ATS is expressed as a part of LNCAT mainly from the paternal allele in the central nervous system (CNS). The transcript is about 450 kbs long, starts at the U-exons and extends as far as UBE3A on the opposite strand, possibly beyond. The promoter for Snurf / Snrpn and

2356-421: The extra chromosome is very small and has no effect on a person's health. A larger isodicentric chromosome 15 can result in weak muscle tone (hypotonia), intellectual disability, seizures, and behavioral problems. Signs and symptoms of autism (a developmental disorder that affects communication and social interaction) have also been associated with the presence of an isodicentric chromosome 15. Other changes in

2418-463: The father and are therefore inactive in the brain. About 10% of Angelman syndrome cases are caused by a mutation in the UBE3A gene, and another 3% result from a defect in the DNA region that controls the activation of the UBE3A gene and other genes on the maternal copy of chromosome 15. In a small percentage of cases, Angelman syndrome may be caused by a chromosomal rearrangement called a translocation or by

2480-407: The formation of this reactive thioester, and subsequent steps are thermoneutral. Next, a transthiolation reaction occurs, in which an E2 cysteine residue attacks and replaces the E1. HECT domain type E3 ligases will have one more transthiolation reaction to transfer the ubiquitin molecule onto the E3, whereas the much more common RING finger domain type ligases transfer ubiquitin directly from E2 to

2542-404: The gene count estimates of human chromosome 15. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction ). Among various projects, the collaborative consensus coding sequence project ( CCDS ) takes an extremely conservative strategy. So CCDS's gene number prediction represents

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2604-401: The idea that Ube3a-ATS might be involved in paternal Ube3a silencing, other studies contradict this. One study in particular argues against the in cis silencing of Ube3 a by Ube3a-ATS . In this study, when the maternal Ube3a allele was deleted, an increase in paternal Ube3a-ATS expression was seen. This suggests that rather than the paternal Ube3a-ATS controlling paternal Ube3a ,

2666-418: The locations and the lengths of the Ube3a-ATS transcripts. The human Ube3a/Ube3a-ATS is located on chromosome 15 , while the mouse Ube3a is located on chromosome 7. The mouse LNCAT , including Ube3a-ATS , is about 1000 kb long, much longer than the human 450 kb LNCAT . Due to the similar organization of the mouse and human LNCAT/Ube3a-ATS and the fact that the mouse Ube3a locus is also imprinted ,

2728-451: The maternal Ube3a allele is inactive, the paternal allele is intact but epigenetically silenced. If unsilenced, the paternal allele could be a source of active Ube3a protein in AS patients. Therefore, understanding the mechanisms of how Ube3a-ATS might be involved in silencing the paternal Ube3a may lead to new therapies for AS. This possibility has been demonstrated by a recent study where

2790-420: The maternal Ube3a somehow suppresses expression of the paternal Ube3a-ATs , possibly in trans rather than in cis . An interaction between the maternal and paternal homologous regions of these genes was in fact observed in human and mouse cells during interphase. One mechanism to explain in trans silencing includes an interaction between the paternal Ube3a-ATS RNA and the maternal Ube3a mRNA . It

2852-418: The maternal allele. Silencing of Ube3a on the paternal allele is thought to occur through the Ube3a-ATS part of LNCAT , since non-coding antisense transcripts are often found at imprinted loci. The deletion and/or mutation of Ube3a on the maternal chromosome causes Angelman syndrome (AS) and Ube3a-ATS may prove to be an important aspect in finding a therapy for this disease. While in patients with AS

2914-417: The maternal and paternal alleles. While differential methylation patterns on the maternal and paternal genes are often associated with imprinting, the AS-IC remains unmethylated at both alleles. However, the neighboring PWS-IC is methylated on the maternal allele, but remains unmethylated on the paternal allele. The PWS-IC is suspected of controlling the expression of LNCAT and Ube3a-ATS . In mice where

2976-726: The most part, it is thought that at least some type of Ube3a-ATS is expressed in CNS cells that are imprinted, such as Purkinje cells and hippocampal neurons. However, there is spatiotemporal regulation of both the downstream and the upstream part of this transcript. and Journal of Neuroscience . In mouse embryos, Snurf/Snrpn exons were detected in blastocysts about 7 days post coitem and continued to be expressed throughout development. The Snurf/Snrpn exons are restricted to CNS tissue during development, and only later during adulthood are expressed in other tissue. Ube3a-ATS exons were not detected until 10 days post coitem and their expression

3038-440: The mouse is an excellent model system to study imprinting and the interactions between Ube3a/Ube3a-ATs . In addition, mouse neurons continue to retain their imprinting pattern in culture. While the entire LNCAT transcript, including the Ube3a-ATS transcript may be transcribed, it is often spliced to include and exclude a variety of exons. Different splice variants are expressed in different tissue types and situations. For

3100-768: The paternal allele to make up for the lack of expression from the maternal allele. A one year study was performed with several AS patients. These patients were put on methylation promoting diets that consisted of betaine , metafolin , creatine , and vitamin B12 supplements. However, after one year, methylation patterns in these patients did not change. Another study tested a large library of different drugs, and identified several topoisomerase I and II inhibitors which increased expression of paternal Ube3a in mouse neurons and mice. Topoisomerase inhibitors are widely used as chemotherapeutics and cause replicating cells to undergo apoptosis by inducing double strand breaks that stall

3162-437: The paternal copy of the chromosome and are inactive on the maternal copy. Therefore, a person with a deletion in the paternal chromosome 15 will have no active genes in this region. In about 25% of cases, a person with Prader–Willi syndrome has two maternal copies of chromosome 15 in each cell instead of one copy from each parent. This phenomenon is called maternal uniparental disomy. Because some genes are normally active only on

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3224-473: The paternal copy of this chromosome, a person with two maternal copies of chromosome 15 will have no active copies of these genes. In a small percentage of cases, Prader–Willi syndrome is not caused by a chromosomal rearrangement called a translocation. Rarely, the condition is caused by an abnormality in the DNA region that controls the activity of genes on the paternal chromosome 15. Because patients almost always have difficulty reproducing, Prader–Willi syndrome

3286-427: The phosphate, as shown in the figure to the right. In absence of the phosphate , residues of FBW7 repel the substrate. The presence of oxygen or other small molecules can influence degron recognition. The von Hippel-Lindau (VHL) protein (substrate recognition part of a specific E3 ligase), for instance, recognizes the hypoxia-inducible factor alpha (HIF-α) only under normal oxygen conditions, when its proline

3348-408: The region of overlap, the less efficient the transcription of the sense strand was, indicating that transcription on one strand interferes with the transcription on the other strand. Another study directly monitored collisions between RNAPs transcribing a template using atomic force microscopy. RNAPs were stalled on DNA fragments and collided with other elongating RNAPs. The images showed stalling of

3410-476: The rest of the SCF complex, and a substrate binding domain, which gives the E3 its substrate specificity. Ubiquitin signaling relies on the diversity of ubiquitin tags for the specificity of its message. A protein can be tagged with a single ubiquitin molecule (monoubiquitylation), or variety of different chains of ubiquitin molecules (polyubiquitylation). E3 ubiquitin ligases catalyze polyubiquitination events much in

3472-412: The role of this particular protein is not yet known. Downstream from Snrpn/Snurf and within its introns are sequences for several C/D box snoRNAs . Most C/D box snoRNAs function in non- mRNA methylation . However, recently, one snoRNA on Ube3a-ATS , SNORD 115, has been found to change the alternative splicing of the serotonin receptor 2C pre-mRNA. In addition, this snoRNA has the ability to change

3534-529: The same way as the single ubiquitylation mechanism, using instead a lysine residue from a ubiquitin molecule currently attached to substrate protein to attack the C-terminus of a new ubiquitin molecule. For example, a common 4-ubiquitin tag, linked through the lysine at position 48 (K48) recruits the tagged protein to the proteasome, and subsequent degradation. However, all seven of the ubiquitin lysine residues (K6, K11, K27, K29, K33, K48, and K63), as well as

3596-411: The splicing of five different mRNAs. Among the sequences for the snoRNAs is nested IPW (imprinted Prader-Willi), a non-coding region whose deletion is thought to cause Prader-Willi syndrome . The mouse and human Ube3a-ATS/Ube3a are orthologous and the general organizations of the regions are similar. For example, the mouse locus also contains Snurf/Snrpn , snoRNAs and IPW. The main differences are

3658-513: The substrate to directly relate its biochemical function to ubiquitination . This relation can be demonstrated with TRF1 protein (regulator of human telomere length), which is recognized by its corresponding E3 ligase ( FBXO4 ) via an intermolecular beta sheet interaction. TRF1 cannot be ubiquinated while telomere bound, likely because the same TRF1 domain that binds to its E3 ligase also binds to telomeres. E3 ubiquitin ligases regulate homeostasis, cell cycle, and DNA repair pathways, and as

3720-432: The substrate. The final step in the first ubiquitylation event is an attack from the target protein lysine amine group, which will remove the cysteine, and form a stable isopeptide bond. One notable exception to this is p21 protein, which appears to be ubiquitylated using its N-terminal amine, thus forming a peptide bond with ubiquitin. Humans have an estimated 500-1000 E3 ligases, which impart substrate specificity onto

3782-434: The two RNAPs immediately after the collision, in addition to backtracking of one of the RNAPs. While these studies have not been performed for Ube3a/Ube3a-ATS , the use of atomic force microscopy to monitor transcription at this locus might provide insight as to how Ube3a is actually silenced via Ube3a-ATS . Further studies are still very much necessary to confirm these models for Ube3a . While several studies support

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3844-458: Was also limited to the CNS during development. In general, Ube3a-ATS is detected during the initial stages of neurogenesis while Snurf/Snrpn is expressed in undifferentiated precursor cells and throughout the course of differentiation. There are at least 10 different splice isoforms according to the UCSC genome browser. According to one study, the splice variant that directly overlaps the Ube3a

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